/*
 * Copyright 2006-2018 The MZmine 2 Development Team
 *
 * This file is part of MZmine 2.
 *
 * MZmine 2 is free software; you can redistribute it and/or modify it under the terms of the GNU
 * General Public License as published by the Free Software Foundation; either version 2 of the
 * License, or (at your option) any later version.
 *
 * MZmine 2 is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License along with MZmine 2; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

package net.sf.mzmine.modules.peaklistmethods.identification.mascot;

import net.sf.mzmine.datamodel.impl.SimplePeakIdentity;

public class MascotPeakIdentity extends SimplePeakIdentity {

  /*
   * private static final String PROPERTY_PEPTIDE = "Peptide sequence"; private static final String
   * PROPERTY_MASS = "Mass (Mr)"; private static final String PROPERTY_DELTA = "Delta"; private
   * static final String PROPERTY_SCORE = "Score"; private static final String PROPERTY_MISSES =
   * "Misses"; private static final String PROPERTY_MODIFICATIONS = "Modifications";
   * 
   * /** This class implements PeakIdentity and wrap the information of the peptide assigned to the
   * chromatographic peak.
   * 
   * @param peptide the peptide hit.
   * 
   * @SuppressWarnings("unchecked") public MascotPeakIdentity(final PeptideHit peptide) {
   * 
   * 
   * final StringBuilder name = new StringBuilder(); for (final ProteinHit p :
   * (Iterable<ProteinHit>) peptide.getProteinHits()) { if (name.length() > 0) { name.append(' '); }
   * name.append(p.getAccession()); }
   * 
   * setPropertyValue(PROPERTY_NAME, name.toString());
   * 
   * final HashMap<Integer, String> varMods = new HashMap<Integer, String>(); for (final
   * Modification mod : peptide.getModifications()) { if (mod != null) {
   * varMods.put(mod.getModificationID(), mod.getType() + " (" + mod.getLocation() + ')'); } }
   * 
   * final int[] modSequences = peptide.getVariableModificationsArray(); String modSeqString = "";
   * for (int i = 0; i < modSequences.length; i++) { if (varMods.containsKey(modSequences[i])) {
   * modSeqString += varMods.get(modSequences[i]) + " [" + i + "], "; } }
   * 
   * setPropertyValue(PROPERTY_METHOD, "MASCOT search"); setPropertyValue(PROPERTY_PEPTIDE,
   * peptide.getSequence()); setPropertyValue(PROPERTY_FORMULA, peptide.getSequence());
   * setPropertyValue(PROPERTY_MASS, String.valueOf(peptide.getPeptideMr()));
   * setPropertyValue(PROPERTY_DELTA, String.valueOf(peptide.getDeltaMass()));
   * setPropertyValue(PROPERTY_SCORE, String.valueOf(peptide.getIonsScore()));
   * setPropertyValue(PROPERTY_MISSES, String.valueOf(peptide.getMissedCleavages()));
   * setPropertyValue(PROPERTY_MODIFICATIONS, modSeqString); }
   */

}
